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Sometime after Jonathan's death, Clark was injected with the Limbo drug, a kryptonite-based serum that gave him the chance to "cross over" and see his father. Jonathan informed Clark that he will become a symbol of peace and justice on Earth, and that Lionel knew his secret. He "pushed" Clark back to life, vowing to always be with Clark.
On his nineteenth birthday, Clark saw Jonathan's spirit at his gravestone, and was surprised and confused when Jonathan instructed him to kill Lionel. Jonathan also appeared to Martha, urging her to convince Clark to kill Lionel. However, the apparition was revealed to be a trick by Brainiac: Lionel had become the Kryptonian vessel for Jor-El, and Brainiac attempted to manipulate Clark into eliminating him. Clark discovered Lionel's meeting with Jonathan the night of his death, and almost succeeded in killing him, but Lionel successfully talked him out of it by pointing out that Jonathan would never want Clark to take a life.